MoBPS (version 1.13.1)

ogc.mobps: Breeding function

Description

Function to simulate a step in a breeding scheme

Usage

ogc.mobps(
  population,
  animallist,
  relationship.matrix.ogc,
  depth.pedigree.ogc,
  bve.pedigree.error,
  ogc.target = "min.sKin",
  ogc.uniform = NULL,
  ogc.lb = NULL,
  ogc.ub = NULL,
  ogc.ub.sKin = NULL,
  ogc.lb.BV = NULL,
  ogc.ub.BV = NULL,
  ogc.eq.BV = NULL,
  ogc.ub.sKin.increase = NULL,
  ogc.lb.BV.increase = NULL,
  bve.p_i.list = NULL,
  miraculix = FALSE,
  miraculix.mult = FALSE,
  import.position.calculation = NULL,
  decodeOriginsU = decodeOriginsR,
  nbits = NULL,
  store.sparse = FALSE,
  verbose = TRUE,
  bit.storing = FALSE
)

Value

contributions of each individual in selection

Arguments

population

Population list

animallist

List of individuals to include in ogc

relationship.matrix.ogc

Method to calculate relationship matrix for OGC (Default: "pedigree", alt: "vanRaden", "CE", "non_stand", "CE2", "CM")

depth.pedigree.ogc

Depth of the pedigree in generations (default: 7)

bve.pedigree.error

Set to FALSE to ignore/correct for any pedigree errors

ogc.target

Target of OGC (default: "min.sKin" - minimize inbreeding; alt: "max.BV" / "min.BV" - maximize genetic gain; both under constrains selected below)

ogc.uniform

This corresponds to the uniform constrain in optiSel

ogc.lb

This corresponds to the lb constrain in optiSel

ogc.ub

This corresponds to the ub constrain in optiSel

ogc.ub.sKin

This corresponds to the ub.sKin constrain in optiSel

ogc.lb.BV

This corresponds to the lb.BV constrain in optiSel

ogc.ub.BV

This corresponds to the ub.BV constrain in optiSel

ogc.eq.BV

This corresponds to the eq.BV constrain in optiSel

ogc.ub.sKin.increase

This corresponds to the upper bound (current sKin + ogc.ub.sKin.increase) as ub.sKin in optiSel

ogc.lb.BV.increase

This corresponds to the lower bound (current BV + ogc.lb.BV.increase) as lb.BV in optiSel

bve.p_i.list

XXX

miraculix

XXX

miraculix.mult

XXX

import.position.calculation

XXX

decodeOriginsU

XXX

nbits

XXX

store.sparse

XXX

verbose

Set to FALSE to not display any prints

bit.storing

Set to TRUE if the MoBPS (not-miraculix! bit-storing is used)

Examples

population <- creating.diploid(nsnp=1000, nindi=100, n.additive = 10)
population <- breeding.diploid(population, breeding.size=100, selection.size=c(25,25),
ogc = TRUE)